The pontiff offered his personal support ahead of a special ceremony at St John the Baptist Cathedral in Norwich over the weekend which was attended by approximately 1,500 people.
His message reads: "His Holiness prays that you may all be renewed in your love of Christ and, in turn, revitalize your parishes, so that all may be 'a community of communities, a sanctuary where the thirsty come to drink in the midst of their journey and a centre of constant missionary outreach' (Evangelii Gaudium 28).
"In this way, you will manifest God's love and mercy to the broader community and share the richness of our faith in Christ Jesus."
A Mass of Thanksgiving at St John the Baptist Cathedral on Saturday was attended by the Vatican's UK representative Archbishop Antonio Mennini, the Bishop of East Anglia Rt Revd Alan Hopes and Archbishop of Westminster Cardinal Vincent Nichols.
Cardinal Nichols said: "The Cathedral houses the images of three East Anglian saints of the first millennium: St Felix, St Etheldreda and St Edmund: a bishop, an abbess and a king.
"They remind us that faith in these parts is as old as the hills. And they offer us a challenge to be diligent in our mission to live out the faith, playing our part in the continuing story of Christianity in East Anglia now and into the future."
Bishops, civic leaders and members of congregations across Norfolk, Suffolk, Cambridgeshire and Peterborough were among guests who could also enjoy a piece of anniversary birthday cake.
Bishop Alan added: "In the 2,000 year history of our Church, our 40 years may seem rather small and insignificant but, of course, these few years mark not only a beginning but also a fruition of a long period of evangelisation and Christian witness in this part of England.
"Over the past 40 years, the Diocese has made its mark in the life of the whole Christian community, in its involvement with and outreach to the neediest and most vulnerable in our society.
The Diocese of East Anglia was established when Pope Paul VI approved its creation and, on June 2, 1976, Bishop Alan Clark was installed as its first bishop.